Miscellaneous

1. Central Pattern Generator Controller - To see the CPG network, navigate to data/locomotion_network/ and run $ python locomotion.py - Please refer to FARMS Network to learn more about how to design new neural network controllers.

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2. Blender Model - To visualize the biomechanical model, first install Blender. - After installation, navigate to data/design/blender and open neuromechfly_full_model.blend with Blender.

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3. Reproducing the Figures - All of the plotting functions used in the paper can be found in NeuroMechFly/utils/plotting.py. Please refer to the docstrings provided in the code for the details about how to plot your simulation data. - For example, for reproducing plots on Fig. 5 and 6 panel E, first, run the script run_kinematic_replay or run_kinematic_replay_ground, and then use:

from NeuroMechFly.utils import plotting
import pickle

path_data = /path/to/kinematic/replay/results/folder

# Selecting right front leg for plotting (other options are LF, RM, LM, LH, or RH)
leg = 'RF'

# Read angles from file
with open(path/to/angles, 'rb') as f:
    angles = pickle.load(f)

# Defining time limits for the plot (seconds)
start_time = 3.5 # 0.5 for grooming
stop_time = 4.6 # 2.5 for grooming

plotting.plot_data(path_data,
           leg,
           angles=angles,
           plot_angles=True,
           plot_torques=True,
           plot_grf=True,
           plot_collisions=True, # For grooming example
           collisions_across=True,
           begin=start_time,
           end=stop_time)

• For reproducing gait/collision diagrams from Fig. 5 and 6, first, run the script run_kinematic_replay or run_kinematic_replay_ground, and then use:

from NeuroMechFly.utils import plotting

path_data = /path/to/kinematic/replay/results/folder

# Selecting walking behavior
behavior = 'walking'

# Defining time limits for the plot (seconds)
start_time = 3.5 # 0.5 for grooming
stop_time = 4.6 # 2.5 for grooming

plotting.plot_collision_diagram(path_data,
                        behavior,
                        begin=start_time,
                        end=stop_time)

• For reproducing plots from Fig. 7 panel E, first, run the script run_neuromuscular_control, and then use:

from NeuroMechFly.utils import plotting

path_data = /path/to/neuromuscular/control/results/folder

# Selecting right front leg for plotting (other options are LF, RM, LM, LH, or RH)
leg = 'RF'

# Defining time limits for the plot (seconds)
start_time = 1.0
stop_time = 1.5

plotting.plot_data(path_data,
           leg,
           plot_angles=False,
           plot_torques=False,
           plot_grf=False,
           collisions_across=False,
           plot_muscles_act=True,
           plot_torques_muscles=True,
           plot_angles_sim=True,
           begin=start_time,
           end=stop_time)